Variant Details Germline Small¶
To open the variant details page, click 'View details' button on your chosen variant in the variant list.
On this page you can:
- Review the QC information for a variant
- Review additional annotations such as population frequencies and ClinVar
- Link out to IGV
- Flag a variant
- Add a variant for export
- Add a comment and or classification to a variant
Variant and Quality Information¶
This panel allows you can view variant coordinates and quality metrics. You can also link out to view the variant in IGV
Key
| # | Section | Description |
|---|---|---|
| 1 | GRCh38 coordinates | The chromosome and position of the variant. |
| 2 | Ref > alt allele | Ref and alt alleles. |
| 3 | Variant allele frequency | Not applicable to germline variants. |
| 4 | Alt allele/total read depth | Number of reads supporting alt allele and total total number of reads. |
| 5 | VCF Filter | Shows whether the variant has passed the variant caller filters. For variants that haven’t passed, the reason is shown in red e.g. ‘DRAGENHardQUAL’ Set if true:QUAL<10.4139. |
| 6 | QC Flags | Flags that indicate a variant call may be of a lower quality and at greater risk of being a false positive. Hover over the QC flag for a description. See QC flags tab for more information. |
| 7 | View in IGV | Click this to open the variant in IGV |
Interpretation¶
This panel allows you to flag, classify, comment and export variants. Please refer to the Recording Interpretation documentation for more details.
Gene information¶
This panel allows you to view information about genes and transcripts that overlap this variant.
It includes:
- Mode of action as listed in Cancer Gene Census (e.g. Oncogene, Tumor suppressor).
- Tier as assigned by the Genomics England pipeline (see Cancer Genome Analysis Guide).
- The HGVS CDS and predicted protein change and consequence for each transcript.
Transcripts
By default, the canonical transcript is shown. But additional transcripts can be viewed by clicking 'Show alternative transcripts'.
Key
| # | Section | Description |
|---|---|---|
| 1 | Affected gene | HGNC Gene symbol. |
| 2 | Mode of action | Mode of action as defined in Cancer Gene Census (Oncogene, Tumor Suppressor gene, Ambiguous) |
| 3 | Tier | Tier as assigned by the Genomics England pipeline (see Cancer Genome Analysis Guide) |
| 4 | Transcript ID | Ensembl Transcript ID. |
| 5 | CDS Change | Coding sequence change (HGVS). |
| 6 | Protein ID | Ensembl Protein ID. |
| 7 | Protein change | Predicted protein change (HGVS) |
| 8 | Predicted consequence | Predicted consequences (SO terms) e.g. Missense variant |
| 9 | Alternative transcripts | Expandable table showing alternative (non-canonical) transcripts |
Population Frequencies¶
Shows the population germline allele frequency obeserved in gnomAD and internal Genomics England dataset.
Tip
By default the overall gnomAD frequency is displayed, but subpopulations can be viewed by clicking 'Show subpopulations'.
Warning
NOTE that this data is taken from a snapshot of gnomAD. The gnomAD version the snapshot was taken from is shown at the top of the section (e.g. 2.0.1). To view the latest gnomAD data, visit the gnomAD website.
Classification databases¶
Lists any matching entries in ClinVar, along with the interpretation, review status and number of submissions.
Warning
NOTE that this data is taken from a snapshot of ClinVar. The year and month (YYYY-MM) the ClinVar snapshot was taken is shown at the top of the section.
Tip
To view the latest ClinVar data, click the 'View in ClinVar' button to link out to the variant page on the ClinVar website in a new tab.
QC Flags¶
Description of the possible QC flags for somatic small variants:
| QC Flag | Description |
|---|---|
| T | the variant is in the final 10% of the coding region and the impact of protein truncation regarding pathogenicity should be evaluated |